This week's video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week's tool is the final piece that you need to know about if you want to create the kind of interaction/network diagrams used in the modeling of a system that I covered last week. The yEd Graph Editor is different than some of the tools. As a corporate product, it doesn't have [caption id="attachment_20574" align="alignright" width="250"] yFiles layouts options in Cytoscape[/caption] the kind of scientific... MORE

The immune system is challenging to study. Different people may mount different responses to assaults on their system--and sometimes the systems go into overdrive on stuff they shouldn't. Cracking the details of the functions of the immune system could help us to combat actual pathogens better, and might also help us to tune down inappropriate responses. The developers of the InnateDB resource hope to help researchers learn more about the relevant genes, pathways, and systems to wrangle the responses. The InnateDB team has been building their resource for years, and the growth of the informatio... MORE

A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips: RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials for IMP are available from: http://t.co/zvlVmoph This week I have claimed Mary's "collected" tip idea & will be featuring one of their videos as this week's quick tip. The Integrative Multi-species Prediction (IMP) web server is a gene-gene network analysis resource. There are several such resources (Cytoscape, IntAct, MINT, STRING, VisANT, and one of my personal favorites GeneMania) that OpenHel... MORE

Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can't. I make my grandpa's recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December. Oh, that's not what this tip is about, it's about database of orthologous groups of genes, eggNOG. We've mentioned eggNOG before several times, but only in passing or in relation (orthologous? :D) to another database or tool. Today, in perfect timing for the season, thought I'd do a quick tip to introduce eggNOG. eggNOG is... MORE

Over 2 years ago I did a tip of the week on Phosida (links to Phosida). Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools (prediction and motif analysis). You can read more about those changes in this year's NAR database issue article. Today's tip will revisit the database and redo a search that was done in the tip from 2009, this time using a prot... MORE

In this week's tip I'd like to introduce you to VirusMINT. We found VirusMINT during our 'regularly scheduled' update of our Introductory tutorial on MINT, or the Molecular INTeraction database. We really like MINT for all the great interaction information they provide on a wide variety of species. When we saw they had a 'virally focused' database, we had to check it out. It turns out that VirusMINT is really unique in that it shows interactions BETWEEN human and viral proteins, all on the same interaction map. PLUS, from the VirusMINT homepage description: VirusMINT uses the PSI-MI standard a... MORE

For this week's tip of the week I'm going to introduce iRefWeb, a resource that provides thousands of data points on protein-protein interactions. If you follow this blog regularly, you may remember that we had a guest post from the iRefWeb team not too long ago. It was a nice overview of many of the important aspects of this tool, and I won't go into those again here--you should check that out. Andrei knows those details quite well! And at the time we also mentioned their webinar was coming up. We were unable to attend that, though, because we were doing workshops at The Stowers Institute. I... MORE

This week's tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? And the next question people have after that is: and where are they expressed? BioGPS can help you with both of those problems. It is a tool that integrates and displays many types of data that researchers would be interested in. It also allows you to customize your display with the types of data that are most relevant to you--using their extensive plug-in collection. And it can do so from your brow... MORE

We spend a lot of time exploring genomic data, variations, and annotations. But of course a linear perspective on the genes and sequences is not the only way to examine the data. Understanding the pathways in which genes and molecular entities interact is crucial to understanding systems biology. There are a number of tools which can help you to visualize and explore this kind of data. KEGG is one of the most venerable tools in bioinformatics, BioCyc is well known and used, Reactome is one of our favorites. Recently NCBI BioSystems has come along, and the BioModels tool at EBI provides more da... MORE

For this week's tip of the week we'll be looking at the Gaggle Genome Browser. As we are seeing more and more species or individuals data coming along from high-throughput sequencing projects, metagenomics data sets, and additional annotation track types coming from various projects--we're gonna need more visualization options. Gaggle Browser provides the foundation for a new kind of visualization and interaction with the data. The Gaggle Browser is one piece of the Gaggle components, actually. Gaggle is actually a framework that enables different enabled tools to interact with each other. If... MORE

We've long been fans of the tools developed by the team responsible for MINT: Molecular INTeraction database. MINT is a curated resource full of experimentally verified protein-protein interactions, with some great visualization options. In addition to the main MINT interface, there are other aspects to the site that bring other types of visualization as well. We have done a tip on MINT in the past, but we wanted to re-visit this for our SciVee collection, and also mention a handy tool called Connect. Connect can be used to enter a list of up to ~100 proteins and generate the connection map... MORE

In today's tip I'd like to introduce you to the Cancer Genome Workbench, or CGWB. The workbench gathers cancer information from a wide variety of projects including Johns Hopkins University and GlaxoSmithKline Cancer Cell Line Genomic Profiling Data, NCI's Therapeutically Applicable Research to Generate Effective Treatment (TARGET), NHGRI's Tumor Sequencing Project (TSP), The Cancer Genome Atlas (TCGA), and the Sanger Center's COSMIC initiative and presents the cumulative data as high-level summary visualizations. The CGWB's genome-browser view is built on a UCSC Genome Browser backbone, for p... MORE

I recently read an article in Science entitled "Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions" written by Choudhary et al. The research uses "high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins" and "demonstrate[s] that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications." I'm going to admit, I know little of acetylation as a regulatory mechanism, though after reading through the paper, I found this quite and interesting find and it suggests t... MORE

MINT, the Molecular INTeraction Database, is so much fun to use. I know--there is high-quality curated information from the scientific literature. And that's the real point. But quite frankly, I just love to examine the protein-protein interactions in the MINT viewer. In this brief (about 3 minutes) exploration of some of the high-level features of MINT I will offer a taste of how fun and informative this resource is. A team at the University of Rome brings MINT to you. Check it out here: http://mint.bio.uniroma2.it/mint/ But at just a few minutes, we can't provide the full detail about how to... MORE

For the 299 resources that matched your query, there are 9 sponsored OpenHelix tutorials available. Click on the icons below to display detailed information on each tutorial.